Abstractα‐Peptoids are peptido‐mimetic foldamers based on poly‐N‐substituted glycines that currently receive a growing interest due to their larger structural diversity, easier synthetic pathways, and larger thermal stability compared to peptides. An appropriate side chain appended to the nitrogen atoms is often crucial to constrain the peptoids into well‐defined and active rigid structures for applications. To shed light on the secondary structure of peptoids, accurate methods for structural characterization are mandatory and typically involve the association of circular dichroism and nuclear magnetic resonance spectroscopies. Molecular simulations can also prove highly complementary to rationalize the relationship between their primary and secondary structures, although much less studies have been reported to date compared to the knowledge accumulated on peptides. To this end, the PEPDROID force field has been developed based on the DREIDING force field, by incorporating a new set of parameters relative to (α and β) peptoids bearing different side chains. The ability of PEPDROID to assess the secondary structure of peptoids by generating Ramachandran‐like plots matching those previously obtained at a quantum‐chemical level for model systems has been demonstrated. For further sake of validation, it is demonstrated that PEPDROID can reproduce the experimental structures of either α‐ or β‐peptoids.

The globular shape of gaseous ions, resulting from the ionization of large molecules such as polymers and proteins, is a recurring subject that has undergone a renewed interest due to the advent of Ion Mobility Spectrometry (IMS), especially in conjunction with theoretical chemistry techniques such as Molecular Dynamics (MD). Globular conformations result from a fine balance between entropy and enthalpy considerations. For multiply charged ions isolated in the gas phase of a mass spectrometer, the coulombic repulsion between the different charges tends to prevent the ions from adopting a compact and folded 3D structure. In the present paper, we intimately associate data from IMS experiments and MD simulations to unambiguously access the conformations of dendrimer ions in the gas phase with a special attention paid to the dendrimer structure, the generation and the charge state. Doing so, we here combine a set of structural tools able to evaluate the (non)globular shape of ions based on both experimental and theoretical results. 2 Scheme 2: Structure of a poly(amidoamine) dendrimer of generation 2 with an ethylene diamine core (EDA), or with a cystamine core (CYS) (see in the box). The layers of generation 0 (green), 1 (blue), and 2 (red) are highlighted. Note that generation 0 for PAMAM dendrimers corresponds to the generation 1 for PPI.

Collagen has a triple helix form, structured by a [-Gly-Xaa-Yaa-] repetition, where Xaa and Yaa are amino acids. This repeating unit can be post-translationally modified by enzymes, where proline is often hydroxylated into hydroxyproline (Hyp). Two Hyp isomers occur in collagen: 4-hydroxyproline (4Hyp, Gly-Xaa-Pro, substrate for 4-prolyl hydroxylase) and 3-hydroxyproline (3Hyp, Gly-Pro-4Hyp, substrate for 3-prolyl hydroxylase). If 4Hyp is lacking at the Yaa position, then Pro at the Xaa position should remain unmodified. Nevertheless, in literature 41 positions have been described where Hyp occurs at the Xaa position (?xHyp) lacking an adjacent 4Hyp. We report four additional positions in liver and colorectal liver metastasis tissue (CRLM). We studied the sequence commonalities between the 45 known positions of ?xHyp. Alanine and glutamine were frequently present adjacent to ?xHyp. We showed that proline, position 584 in COL1A2, had a lower rate of modification in CRLM than in healthy liver. The isomeric identity of ?xHyp, that is, 3- and/or 4Hyp, remains unknown. We present a proof of principle identification of ?xHyp. This identification is based on liquid chromatography retention time differences and mass spectrometry using ETD-HCD fragmentation, complemented by ab initio calculations. Both techniques identify ?xHyp at position 584 in COL1A2 as 4-hydroxyproline (4xHyp).

The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH4 + from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH4 + or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.

Animal venoms are a rich source of pharmacological compounds with ecological and evolutionary significance, as well as with therapeutic and biotechnological potentials. Among the most promising venomous animals, cone snails produce potent neurotoxic venom to facilitate prey capture and defend against aggressors. Conus striatus, one of the largest piscivorous species, is widely distributed, from east African coasts to remote Polynesian Islands. In this study, we investigated potential intraspecific differences in venom composition between distinct geographical populations from Mayotte Island (Indian Ocean) and Australia (Pacific Ocean). Significant variations were noted among the most abundant components, namely the κA-conotoxins, which contain three disulfide bridges and complex glycosylations. The amino acid sequence of a novel κA-conotoxin SIVC, including its N-terminal acetylated variant, was deciphered using tandem mass spectrometry (MS/MS). In addition, the glycosylation pattern was found to be consisting of two HexNAc and four Hex for the Mayotte population, which diverge from the previously characterized two HexNAc and three Hex combinations for this species, collected elsewhere. Whereas the biological and ecological roles of these modifications remain to be investigated, population-specific glycosylation patterns provide, for the first time, a new level of intraspecific variations in cone snail venoms.